"Seeds won't sprout - which really sucks because I would have liked to have started to grow some food. I'm not really much of a fruit and vegetable guy, but anything would be better than the crap that you've been serving us. And there's not enough water, and the beds are rock hard and, oh, don't let me forget to mention that I was shot by one of your people!"

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In 2009, he was at Icarus Base, when it fell under attack by what some people suspect were Lucian Alliance. Instead of gating back to Earth, Dr.Nicholas Rush dialed the nine chevron address, which sent Franklin, among others to the Destiny, an Ancient starship. He was assigned a team to search the ship while the life support system was failing. After finding a leak among a compromised Ancient shuttle. Since the airlock can only be closed from the inside, Franklin was asked to repair the system from the outside. Despite numerous attempts, he could not find a way to shut it down. One of the pressures he dealt with was when SenatorAlan Armstrong held him and MSgt.Ronald Greer at gunpoint, demanding to get into the shuttle and close it manually. Not wanting someone to sacrifice himself, he kept trying to close off the area, but he then admitted he cannot close it. He witnessed Armstrong sacrifice himself to save everyone on the ship for at least 24 hours.

Later, Rush apparently "told" the ship about the life support problem, and in response, the ship flew within Stargate range of a desert planet, which contained a mineral required to repair the CO2 scrubbers. Franklin was one of seven people (others being Greer, Rush, Andrea Palmer, Curtis, Lt. Matthew Scott and Eli Wallace) selected to go to the planet. On the planet, he teamed up with Sgt.Curtis, Andrea Palmer and Eli Wallace, while Lt.Matthew Scott, Greer and Rush went elsewhere. After a fruitless search for the lime they seek on repairing the CO2 scrubbers, Franklin, Curtis and Palmer elected to dial one of the other four planets relatively near Destiny's range, even though Rush said the planets were locked out for a reason. They chose not to listen and go ahead. Franklin had the team's only remote control, and leaving the planet would strand the rest of the expedition. By the time Greer and Rush arrived, Curtis and Palmer already went through the Stargate. Before Franklin could leave, Greer shot him in the shoulder. He was later taken back on board the Destiny, where his wounds were treated by Lt.Tamara Johansen. (SGU: "Air, Part 1", "Air, Part 2", "Air, Part 3")

During his recovery, and after power failed on the ship, he asked Eli Wallace why the power failed, though he didn't have the answers. After Destiny recharged itself, he noticed the lights turning back on, and asked ColonelEverett Young why it came back on, but he too had no answers. (SGU: "Darkness", "Light")

A few days later, half the ship's water reserves were depleted by the swarmLt.Matthew Scott unknowingly brought back with him from the desert planet. Before the crew were made aware of this, Franklin believed the military population have hoarded the supplies to control the civilian population. Later, he noticed MSgt.Ronald Greer searching Chloe Armstrong's quarters to see if anyone stole the water. He resented the search, but this provoked Greer to search his quarters next. He later attempted to complain about Greer's attitude to ColonelEverett Young. However, Young seemed to ignore him, as did other issues from Dr.Lisa Park and Dr.Dale Volker. (SGU: "Water")

Sometime after a team went to the Jungle planet, Franklin decided to start a Hydroponics lab on the ship to grow some fresh fruits and vegetables, to replace the rations he found distasteful. However, at first, nothing would grow. Also, he was one of the first people to undergo a Psychiatric evaluation by Lt.Tamara Johansen. He was also forced to undergo fitness sessions lead by Lt.Matthew Scott, but found them difficult, especially when Sgt.Spencer was in charge. He later innocently bumped into Spencer, whose attitude by then had deteriorated. Despite being apologetic, Spencer went into an altercation with him, but was stopped abruptly by ColonelEverett Young. He returned to the hydroponics lab after the incident and was happy to see one of the seeds starting to grow. (SGU: "Life")

When ColonelEverett Young was forced to step down from command of Destiny due to being prime suspect in the murder of Sgt.Spencer, Camile Wray was put in charge. Wray gave Dr.Nicholas Rush permission to head a research team which included Franklin. The team's primary focus was the Destiny interface chair. Franklin was working alone on a late shift when Eli Wallace entered the room. After a brief conversation, he asked Eli to bring him some food. In the time that Eli was gone, despite implicit orders not to use the device, Franklin sat in the chair. When Eli returned, he found Franklin convulsing in the chair, with the device's electrodes cut into his temples. Unable to remove Franklin from the device, Eli called for help. When the device finally disconnected itself, Franklin fell to the floor convulsing and later went into a deep catatonic state. Wray, while still in charge ordered Lt.Tamara Johansen to give Franklin a high dose of Lorazepam, despite not knowing what effects it may have, if any. Franklin's was still in a coma as of the second time the interface device was used. (SGU: "Justice", "Human")

Later, when Destiny entered the void between two galaxies, Franklin awoke from his coma but was still unresponsive. When one of the ship's Faster-Than-Light engine was sabotaged, he was cared for by Lt.Vanessa James as many people were hurt during the explosion and the infirmary was overrun with injured expedition members. James believed Franklin to be more aware than was made apparent and as she fed him, she explained the situation. During this time, the Nakai race managed to locate Destiny and began an attack. Franklin struggled, but managed to speak, telling her "the chair", which prompted her to interrupt Dr.Nicholas Rush and ColonelEverett Young as Young was about to use the Destiny interface chair. They instead asked Franklin to sit in the chair for a second time, to which he agreed. As he connected to the device, cold air was pumped into the room, rapidly reducing the temperature. Young ordered Sgt.Hunter Riley to guard the door to the room as he went to deal with the insuing attack. However, the battle was short as Franklin soon commanded the ship to re-enter FTL. When Young returned to the room, Franklin had disappeared as the ship downloaded his consciousness into the mainframe. Young ordered a search, but eventually called it off. (SGU: "Sabotage", "Pain", "Hope")

In an alternate timeline, he and several others traveled to the Jungle planet. During the first night, half the team were brutally killed by Squigglers, but Franklin was able to survive. However, he became ill from the virus from some of the water that wasn't purified properly from Hoth. By the second night, the rest of the team were killed, but by then, Franklin already succumbed to the pathogen. (SGU: "Time")

In another alternate timeline, when the team found an old Kino, they avoided the planet until they determined the venom from the Squigglers served as some kind of cure for the virus. However, the Franklin of that reality became ill, and before an away team unsuccessfully collected a live specimen, Franklin was one of the first four to have died. (SGU: "Time")

It would seem that per the episode "Life", Franklin is a botanist, or at least has some knowledge about the subject.

Joseph Mallozzi stated in his blog that Destiny had "absorbed" Franklin and uses his brain patterns as a template for the Destiny AI to operate which gives the AI information on what humans need and feel.